To change the marker size just change the values where they are defined in each file describing missions. Alternatively, ifyou want all markers the same size you can set the size in GMS_fnc_spawnMarker.
The version / build are logged in your server.rpt. The location of the file depends a bit on how your server is set up. On Epoch servers it is usually stored in the SC folder. A new file is generated after each restart (thank goodness for that - thank you Bohemia).
You can also directly check the build in the custom_folder\init folder - just look for a file called build.sqf.

From your SC directory send the most recent file named arma3serverXXXXXX.RPT (where the xxxxxx's correspond to a time-stamp).
From your computer's %appdata%\local\arma3 folder send arma3XXXXXX.RPT.
are you using the install guide from DirtySanchez?

You have not given me much information to go on. Could you describe the problem in detail please including what mod (epoch or exile) and what you have done to troubleshoot so far?
I have not had any trouble accessing crates. remember that loot may not be loaded until mission completion depending on how you set things up.

I have been going through this and found a few scripting errors. I believe all have been corrected. Below is a link to the updated pbo. Thanks for reporting the issues and for your patience. This version will be merged with the Main Branch as Version 1.80 build 118.
https://www.dropbox.com/s/6op9nrvixue4kq6/custom_server.pbo?dl=0

Added some new features to the experimental branch Build 118
1. Added listings of armed vehicles you can use to easily customize vehicle patrols based on mission difficulty.
2. Added a few settings by which you can specify the distance between missions, players, bases and towns.
3. did a bit of debugging and script optimization.